title: UMI-RNAseq for  NIH3T3 cell line

city: wuhan

first: li

last: dong

address: hongshan

institute: Huazhong University of Science and Technology

summary:
Purpose: To analyze the sensitivity and specificity of the AmpFISH method, we sequenced the NIH3T3 cell line via UMI-RNAseq experiments.
Methods:NIH3T3 cells were grown in DMEM (Dulbecco’s Modified Eagle Medium, Gibco) supplemented with 10% FBS (Fetal Bovine Serum, Sigma), 50U/ml Penicillin and 50 mg/ml streptomycin (Gibco,cat.no.15070) at 37℃ with 5% CO2. Cells were treated with 0.25% trypsin solution (HyClone, No.SH42605.01) when they reached ~106 cells/ml. Then, the cells were washed with 1X PBS, and then mixed with 1ml TRIzol solution (ThermoFish, No.15596029), and snap-frozen with dry ice. Total RNA was qualitatively and quantitatively evaluated as follows:
(1) the RNA sample was initially qualitatively evaluated using 1% agarose gel electrophoresis for possible contamination and degradation;
(2) RNA purity and concentration were then examined using NanoPhotometer spectrophotometer;
(3) RNA integrity and quantity were finally measured using RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system. After library preparation and pooling of different samples, the samples were subjected to Illumina sequencing. The libraries were sequenced using the Illumina NovaSeq 6000 Platform for 6G raw data and generated 150nt pair-end reads. UMI sequences on each read were identified by UMI-tools (1.0.0), and reads with UMIs were used for the subsequent analysis. To identify the duplicated reads, UMIs were initially removed from the UMI reads, and the remaining parts of each read were mapped to the reference genome using Hisat2. Reads that mapped to the same location on the reference genome were identified as duplicated reads. Then, the UMIs on each read were recalled, and the duplicated reads with the same UMI were identified as non-natural duplications, which were subsequently removed from the processed data. HTSeq v0.6.1 was used to count the read numbers mapped to each gene. Then, the FPKM of each gene was calculated based on the length of the gene, and the read count was mapped to the gene.
Conclusions:AmpFISH provides convenient and versatile tools for sensitive RNA/DNA detection and to gain useful information on cellular molecules using simple workflows

overall_design: we introduce a method to prepare long single-strand DNA concatemers (lssDNAc) through a controllable rolling-circle amplification (CRCA). Prepared lssDNAcs were used to develop novel AmpFISH workflows.

first: Dongjian

last: Cao

first: Sa

last: Wu

first: Caili

last: Xi

first: Dong

last: Li

first: Kaiheng

last: Zhu

first: Zhihong

first: Hui

last: Gong

first: Qingming

last: Luo

first: Jie

last: Yang


title: Genome-wide identification of RNA-chromatin interactions in Arabidopsis [GRO-seq]

status: Public on Aug 10 2021

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

country: China

institute: Tsinghua University

summary: It is increasingly evident that various RNA molecules can bind chromatin to regulate gene expression and genome organization. Here we adapted a sequencing-based technique to profile RNA-chromatin interactions at a genome-wide scale in Arabidopsis seedlings. We identified more than ten thousand RNA-chromatin interactions mediated by protein-coding RNAs, long non-coding RNAs (ncRNAs) and small ncRNAs in Arabidopsis. These RNAs preferentially target genic regions, especially exonic regions. Protein-coding RNAs primarily engage in local and cis-chromosomal interactions, whereas long ncRNAs (lncRNAs) and small ncRNAs preferentially engage in trans-chromosomal interactions. RNA-chromatin interactions tend to positively correlate with DNA-DNA interactions, suggesting a role of DNA-DNA interactions in confining RNA-chromatin interactions and/or a role of RNA-chromatin interactions in shaping genome organization at a global level. We further show that some RNA-chromatin interactions undergo alterations in response to biotic and abiotic stresses. Our study provides a global view of RNA-chromatin interactions in Arabidopsis and a rich resource for future investigation of the regulatory roles of RNAs in gene expression and genome organization.

overall_design: To identify chromatin-associated RNAs and their target sites in Arabidopsis, we conducted GRID-seq using Arabidopsis wild-type Col-0 seedlings. To evaluate the contribution of RNA transcription level to the abundance of RNAs detected in GRID-seq, we conducted global nuclear run-on sequencing (Gro-seq) to detect the levels of nascent RNAs and compared RNA reads in GRID-seq and Gro-seq. To determine the overlap between RNA-chromatin interactions and DNA-DNA interactions, we conducted BL-Hi-C and compared interactions identified by GRID-seq and BL-Hi-C. To determine whether RNA-chromatin interactions are dynamic and respond to environmental cues, we conducted GRID-seq using heat-treated and DC3000-treated seedlings.

first: Lanxia

first: Haofei

first: Lu

last: Han

first: Yan


title: A novel therapeutic strategy targeting the mesenchymal phenotype of malignant pleural mesothelioma by suppressing LSD1 [array]

city: Bunkyo-Ku

first: Ken

last: Tajima

state: Tokyo

address: 2-1-1 Hongo

department: Department of Respiratory Medicine

country: Japan

institute: Juntendo University

summary:
Transcriptome analysis following knock down of LSD1 in ACC-MESO-1 cells.
Malignant pleural mesothelioma (MPM) is a highly aggressive tumor that has a low overall survival; however, no significant treatment advances have been made in the past 15 years. In this study we investigated whether targeting lysine-specific demethylase 1 (LSD1/KDM1), a histone-modifying enzyme responsible for demethylating histone H3 lysine 4 and lysine 9, could represent a novel therapeutic strategy for patients with MPM. We found that suppressing LSD1 induces an epithelial phenotype in sarcomatoid MPM cells, while attenuating the mesenchymal phenotype sensitized MPM cells to cisplatin-induced apoptosis through the FAK pathway. To investigate the potential mechanisms underlying FAK pathway activation, we performed transcriptome analysis using two different shRNA constructs against the LSD1.

overall_design: We performed transcriptome analysis in ACC-MESO-1 cells infected with shLSD1 or control using the Clariom S Array platform.

first: Aditya

last: Wirawan


title: The Small RNA sequencing of 12 mammary gland for Chinese Holstein Cattle

status: Public on Aug 11 2021

city: Beijing

first: Wentao

last: Cai

address: No2. Yuanmingyuan West Road

institute: Chinese Academic of Agricultural Science

type: Non-coding RNA profiling by high throughput sequencing

summary: Milk protein is one of the most important economic traits in the dairy industry. Yet, the miRNA gene regulatory network for the synthesis of milk protein in mammary is poorly understood. In this study, the hypothesis was that miRNAs have potential roles in bovine milk protein production. Using miRNA-seq and RNA-seq, we investigated the miRNAs profiles of mammary glands from 12 Chinese Holstein cows with six cows at peak of lactation and six in non-lactating period, from which three cows were in high and three in low milk protein percentage.

overall_design: Based on Dairy Herd Improvement system (DHI) data, the 12 multiparous and healthy mastitis-free Chinese Holstein cattle with three too high and three low phenotypic values for milk protein percentage peak and non-lactation period were chosen from our study, which has been described in the previous study. All mammary samples were retrieved from the 12 candidate Chinese Holstein cows using a biopsy, then placed in liquid nitrogen until RNA isolation.

first: Cong

first: Shengli

last: Zhang

first: Junya


title: Histone deacetylase 1 and 2 drive differentiation and fusion of progenitor cells in human placental trophoblasts

city: London

first: Stephen

middle: James

last: Renaud

state: Ontario

address: 1151 Richmond St

department: Anatomy and Cell Biology

country: Canada

institute: Western University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In this study, we report the acetylation changes during cytotrophoblast cells differentiating into syncytiotrophoblast. We identified several genomic regions in which acetylation patterns are altered during cytotrophoblast differentiation that correlate with the robust changes in gene transcription required during differentiation.

overall_design: Examination of acetylation pattern of cytotrophoblast differentiating into syncytiotrophoblast.

middle: J

first: Gargi

last: Bhattad


title: Acclimation of rice leaves to varying temperatures

city: Brisbane

first: Peter

middle: A

last: Crisp

state: QLD

address: John Hines Building (62), The University of Queensland

department: School of Agriculture and Food Science

country: Australia

institute: The University of Queensland

type: Expression profiling by high throughput sequencing

summary: The extent to which light-saturated net CO2 assimilation (An) and leaf dark respiratory CO2 release (Rdark) jointly acclimate to abrupt and sustained changes in temperature (T) in rice (Oryza sativa L.) is unclear, as are the underlying mechanisms associated with thermal acclimation.  To further our understanding of how sustained changes in temperature affect the carbon economy of rice, hydroponically-grown plants of the IR64 cultivar were developed at 30/25°C (day/night) in a temperature-controlled greenhouse before being shifted to 25/20°C or 40/35°C. Leaf RNA expression, protein abundance, sugar and starch content, gas-exchange and elongation rates were measured on pre-existing leaves (PE) already developed at 30/25°C, or leaves newly-developed (ND) subsequent to temperature transfer.

overall_design: To investigate changes in gene expression following temperature shifts in rice we employed total RNA-seq capturing both poly(A) and non-poly(A) transcripts. Rice plants were grown under control conditions at day/night temperatures of 30/25 °C (”warm”) for 2 weeks, then shifted to either 40/35 °C “hot” or 25/20 °C “cold” treatments. Samples were then collected for RNA-seq at 0 hr, 2 hr, 6 hr and 24 hr time points (n = 4).

first: Andrew

last: Scafaro

first: Oliver

last: Berkowitz

first: James

last: Whelan

first: Owen

middle: K

last: Atkin


title: Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus

status: Public on Aug 13 2021

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

country: United Kingdom

institute: The University of Oxford

summary: To identify a causative variant and effector gene responsible for a 2-fold increased risk of severe COVID-19, a multi-omics platform was deployed. A combination of ATAC-seq, ChIP-seq, Micro Capture-C and NuTi Capture-C were used to characterize a range of cell types, including epithelial, fibroblast, endothelial, immune and erythroid cells.

overall_design:
Micro Capture-C, ATAC-seq and ChIP-seq were deployed in epithelial, endothelial and fibroblast cells to characterize the epigenetic regulatory landscape of 3p21.31 - a locus which confers a 2-fold chance of severe COVID-19

NuTi Capture-C was used in immune, endothelial, epithelial, fibroblast and erythroid cells and can be found at GSE159867.


title: Genome wide chromatin accessibility of Helios null hematopoietic stem and progenitor cells

city: illkirch

first: giovanni

last: cova

address: 1 Rue Laurent Fries

country: France

institute: igbmc

summary: This experiment aimed to determine Helios contribution in chromatin accessibility in hematopoietic stem and progenitor cells. Thus, we examined the change in chromatin accessibility in purified hematopoietic stem cells (LSK, Lin-Sca1+ckit+) from 10 weeks old WT and Helios deficient mice using the ATAC-seq approach. We found that Helios null LSK an affected Open Chromatin Region (OCR) landscape, overall in the proximity of genes regulating platelets functions.

overall_design: ATAQ-seq of hematopoiectic stem and progenitor cells from Helios null and WT mice.

first: Giovanni

last: Cova

first: Peggy

last: Kirstetter

first: Philippe

last: Kastner

first: Susan

last: Chan


title: Targeting the IRE1α/XBP1 endoplasmic reticulum stress response pathway in ARID1Amutant ovarian cancers

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

country: USA

institute: The Wistar Institute

summary: xenograft, patientderived xenograft and the genetic Arid1aflox/flox/Pik3caH1047R mouse models. Finally, B-I09 synergizes with inhibition of HDAC6, a known regulator of the ER stress response, in suppressing the growth of ARID1A-inactivated OCCCs. These studies reveal a promising therapeutic strategy for ARID1A-mutant OCCCs and define the IRE1?-XBP1 axis of the ER stress response as a targetable vulnerability for ARID1A-mutant OCCCs. Our findings indicate that pharmacological inhibition of the IRE1?-XBP1 pathway alone or in combination with HDAC6 inhibition represents an urgently needed therapeutic strategy for ARID1A-mutant ovarian cancers.

overall_design: RNA-seq experiment in ARID1A WT and KO cells under control and tunicamycin treatment

first: Joseph

last: Zundell

first: Rugang


title: Interneuron origin and molecular diversity in the human fetal brain

city: XiaMen

first: yuan

last: yu

state: FuJian

address: JiMei Street, 668

department: Center for precision medicine

institute: HuaQiao university

summary: GABAergic inhibitory neurons are crucial in maintaining the stability of neural circuits through synaptic inhibition in the human brain. In this study, we used single-cell RNA sequencing to profile the transcriptomes of fetal cells collected along an early developmental time course to clarify the origin and diversification of interneurons. The heterogeneity of interneurons within the human subpallium is observed in ganglionic eminence precursors and driven by a string of gene regulatory networks that exhibit evident differences in the subventricular zone during the late first trimester. We identified conserved molecular signatures between the cardinal interneuron subtypes of ganglionic eminence precursors and adult interneurons through comparing embryonic and mature cortex data sets.

overall_design: Single cell sequencing of human fetal subpallium

first: Yuan

last: Yu

first: Tao

last: Sun


title: Analyzing The Effects of ProL1 Upregulation On LNCaP Global Gene Expression

status: Public on Aug 12 2021

city: Bronx

first: Kelvin

middle: Paul

last: Davies

state: New York

address: 1300 Morris Park Avenue, Forchheimer 742

department: Urology

institute: Albert Einstein College of Medicine

summary:
Purpose: To examine the effects of proL1 upregulation on global gene expression in LNCaP cells using RNA sequencing (RNA-Seq)
Methods: LNCaP cells were transformed to overexpress proL1 using lentiviral vectors. The proL1 overexpressing variant (LNCaP proL1+) and their parental cell line were plated in 6-well plates in triplicate (3 wells for each cell line). After 3 days, their RNA was isolated using the Qiagen RNeasy Mini kit and their global gene expression patterns were analyzed using RNA-Seq
Results: We identified 1110 differentially expressed genes between LNCaP proL1+ and its parental cell line. Of these differentially expressed genes (DEGs), 209 were in common with PC3 when proL1 was overexpressed. To identify biological functions that may be regulated through overexpression of proL1 in LNCaP cells, the list of DEGs was submitted to the DAVID, GOC, and KEGG databases. According to these databases, proL1 overexpression regulated gene expression in ontological groups involved in morphogenesis and signal transduction. DEGs were also overrepresented in ontological groups potentially involved in vascularization and blood flow regulation. However, there were differences in the regulation of specific genes related to the androgen response between LNCaP and PC3. Unlike PC3, where overexpression of ProL1 caused a significant increase in expression of the androgen receptor gene (AR) and a decrease in expression of the estrogen receptor (ESR1), in LNCaP neither of these genes were changed in expression. In contrast, proL1 overexpression in LNCaP reduced expression of the progesterone receptor gene (PGR) but not in PC3 cells.
Conclusion: Global analysis of the changes in gene expression caused by proL1 overexpression in PC3 and LNCaP cells supports that it has a role both in the modulation of genetic pathways involved in both overcoming hypoxia and the development of androgen-insensitivity. Opiorphins have previously been shown to be directly involved in regulation of blood-flow to tissues through their modulation of smooth muscle tone, and therefore their upregulation in tumors may directly contribute to overcoming the hypoxic barrier that develops in the growing tumor. In addition, overexpression of ProL1 in both PC3 and LNCaP cells modulated expression of genes involved in angiogenesis and morphogensis; the activation of these pathways would likely be involved in vascularization of the tumor and thereby also contribute to overcoming hypoxia. Overexpression of proL1 also affected genes involved in steroid metabolism and response pathways in both LNCaP and PC3, which could potentially contribute to the modulation of androgen sensitivity. For example, overexpression of ProL1 in LNCaP reduced expression of the progesterone receptor gene (PGR). Activation of PGR is a positive modulator of cell division and the reduced expression of PGR in LNCaP proL1 cells might therefore explain the negative effect on tumor growth in female mice. Overall, our data associates the development of PrCa with overexpression of opiorphin and suggests genetic pathways by which they contribute to tumor growth and development of androgen-insensitivity.

overall_design: Total RNA of LNCaP cells overexpressing proL1 and their parental cell line

first: Amarnath

last: Mukherjee

first: Augene

last: Park

first: Li

last: Wang

middle: P


title: Deficiency of Autism Risk Factor Ash1l in Prefrontal Cortex Induces Genetic Aberrations, Synaptic Imbalance and Severe Seizures

city: Buffalo

first: Zhen

last: Yan

state: NY

address: 955 Main St

institute: SUNY Buffalo

summary: We performed RNAseq experiments to examine genome-wide transcriptional changes in PFC of shRNA-ASH1L KD mice compared to GFP injected control mice.

overall_design: mRNA via RNAseq analysis of three 6-8 week old  shRNA-ASH1L-injected KD mice  (C57BL6/J) , and two 6-8 week old GFP-injected control mice (C57BL6/J) PFC tissue were compared.

first: Jamal

last: Williams


title: Gene expression signatures for Intrahepatic cholangiocarcinoma

status: Public on Aug 09 2021

city: beijing

first: lei

middle: lei

last: liang

address: panjiayuan

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

summary:
CircRNA microarray was used to screen significantly up-regulated circRNAs in paired ICC and non-tumor tissues
7 paired ICC and non-tumor tissues was used to screen significantly CircRNAs

overall_design: 7 paired ICC and non-tumor tissues，We have completed the Arraystar Human circRNA Array v2 analysis of the 14 samples that you submitted. Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array v2 (8x15K, Arraystar). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

first: Feng

last: Shen

first: Qinjunjie

last: Chen


title: Transcriptome analysis following Apigenin and Chrysin treatment of Mouse Embryonic Fibroblasts

city: Downers Grove

first: Prasanth

last: Puthanveetil

address: 555, 31st Street

department: Pharmacology

institute: Midwestern University

summary: There is no known single therapeutic drug for treating hypercholesterolemia that comes with negligible systemic side effects. In the current study, using next generation RNA sequencing approach in mouse embryonic fibroblasts we discovered that two structurally related flavonoid compounds, Apigenin and Chrysin exhibited moderate blocking ability of multiple transcripts that regulate rate limiting enzymes in the cholesterol biosynthetic pathway. The observed decrease in cholesterol biosynthesis pathway correlated well with an increase in transcripts involved in generation and trafficking of ketone bodies as evident by the upregulation of Bdh1 and Slc16a6 transcripts. Impact statement - The hypocholesterolemic potential of Apigenin and Chrysin at higher concentrations along with their ability to generate ketogenic substrate especially during embryonic stage is useful or detrimental for embryonic health is not clear and still debatable. Our findings will set the stage for translating this information to whole animal and clinical studies that could shed light to the existing information regarding safe use of Apigenin and Chrysin, specifically to embryonic health.

overall_design: Evaluation of the effects of two different flavonoids- Apigenin and Chrysin using RNA Seq analysis on Mouse Embryonic Fibroblast cells- in Mus Musculus transcriptome and mm9 genome and files or contents expressed as log 2


title: Targeted transposon screening in bacteria by CRISPR/Cas12k-guided transposase

city: Guangzhou

first: ren

last: zehui

address: No. 135, Xingang Xi Road

institute: SUN YAT-SEN UNIVERSITY

summary: Here, we report a CRISPR/Cas12k-transposon-assisted genome engineering (CTAGE) method that allows for high-throughput site-specific mutagenesis in microbial genomes. Exploiting the powerful CTAGE technique, we construct a site-specific transposon mutant library focusing on all the possible transcription factors (TFs) in Pseudomonas aeruginosa, enabling comprehensive identification of essential genes and new factors for antibiotic resistance.

overall_design: Examination resistance gene of imipenem, ceftazidime and ofloxacin in Pseudomonas aeruginosa.

first: Chen

last: Weizhong

first: Ren

last: Zehui


title: RNA seq of cardiac fibroblasts primary cell lines after stimulation with WNT3a or WNT5a with or without TGFB

status: Public on Aug 08 2021

city: Kraków

first: Przemysław

last: Błyszczuk

address: Wielicka 265

country: Poland

institute: Jagiellonian University

summary: To recognize the influnence of WNT signaling on fibroblasts differentiation first we analyzed transformation of human cardiac fibroblasts caused by TGF-β signaling. Differential gene expression analysis demonstrated that cardiac fibroblasts 72h after treatment with TGF-β showed deregulated expression of 313 genes. We also observed that stimulation with WNT3a resulted in deregulation of 124 genes in TGF-β-treated fibroblasts and in contrast to profound effect of WNT3a on fibroblasts differentiation, treatment with WNT5a  upregulated expression of only 2 and downregulated 21 genes in TGF-β-activated cells.

overall_design: Examination of effect WNT3a and WNT5a on cardiac fibroblasts differentiation

first: Edyta

last: Działo


title: A Genome-Scale TF-DNA Interaction Network for Transcriptional Regulation of Arabidopsis Primary and Specialized Metabolism

city: Davis

first: Michelle

last: Tang

state: California

address: One Shields Avenue

department: Plant Sciences

institute: UC Davis

summary: We measured the transcriptional changes of dark grown seedlings in which CHA19, ENAP1, LBD16 and WRI3 translocation into the nucleus are controlled by a dexamethasone-inducible glucocorticoid receptor to investigate targets of these TFs in the TCA cycle and other sectors of primary metabolism.

overall_design: 35S:CHA19, 35S:GR-ENAP1, 35S:GR-LBD16 and 35S:GR-WRI3 were grown in half-strength MS media for 5 days in the dark and then transferred to media with mock or 10 uM dexamethasone to be treated for 24 hr. mRNA was extracted from whole seedlings for RNA-seq libraries.

first: Daniel

last: Kliebenstein

first: Siobhan

last: Brady


title: PCSK9 is involved in human induced pluripotent stem cell proliferation through the regulation of the NODAL signaling pathway II

status: Public on Aug 07 2021

city: Nantes

first: Antoine

last: Rimbert

address: 8 quai moncousu

institute: Institut du thorax inserm-U1087

summary: Proprotein convertase subtilisin kexin type 9 (PCSK9) is a key regulator of LDL cholesterol metabolism and the target of lipid-lowering drugs. PCSK9 is mainly expressed in hepatocyte. Here, we show that PCSK9 is highly expressed in undifferentiated hiPSCs. PCSK9 inhibition in hiPSCs with the use of shRNA, CRISPR/cas9-mediated knockout or endogenous PCSK9 loss-of-function mutation R104C/V114A unveiled its new role as a potential cell cycle regulator through the NODAL signaling pathway. Indeed, PCSK9 inhibition leads to a decrease of SMAD2 phosphorylation and hiPSCs proliferation. Conversely, PCSK9 overexpression stimulates hiPSCs proliferation. PCSK9 can interfere with the NODAL pathway by regulating the expression of its endogenous inhibitor DACT2, which is involved in the TGFß-R1 lysosomal degradation. Using different PCSK9 constructs we show that PCSK9 interacts with DACT2 through its CHRD domain. Altogether these data highlight a new role of PCSK9 in cellular proliferation and development, beyond its canonical effect on lipid metabolism.

overall_design: PCSK9 gene expression has been silenced upon lentiviral transduction of specific shRNA (Sigma). The clone TRCN0000075236 cloned into the pLKO.1-Puro vector has been used to target PCSK9 (N=3) while an unspecific shRNA sequence has been used as control (N=3). Upon transduction, K3 hiPSC  (Si-Tayeb et al., 2010) were subjected to Puromycin (TOCRIS Bioscience 4089/50) selection using a concentration up to 8µg/ml.

first: Karim

last: Si-Tayeb


title: Gene expression in human cell lines reproducing breast cancer progression

city: PITTSBURGH

first: Camille

last: Jacqueline

address: 200 LOTHROP ST FL10, BIOMEDICAL SCIENCE TOWER, E1000-15B

institute: Univeristy of Pittsburgh

summary:
We looked for difference in genetic expression in 4 cell lines that have the same genetic background but reproduce breast cancer progression. Especially, we identied genes that were overexpressed in late cancer
progression (MCFT1 and MCFCA1) but not in early stages (MCF10A and MCFNeoT).

overall_design: Total RNA was extracted from 4 human cell lines : MCF10A, MCFNeoT, MCFT1 and MCFCA1 and used to performed a Nanostring array (NanoString  nCounter Immunology Panel (Human V2).

first: Olivera

last: Finn


title: miRNAs in MSCs-exosome compared with NIH3T3-exosome

city: Maebashi

first: Akihiko

last: Uchiyama

state: Gunma

department: Dermatology

institute: Gunma university

summary: We report the application of Microarray analysis using micro RNAs in esoxomes from mouse bone marrow derived mesenchymal stem cells (MSCs) and NIH3T3 cells were compared

overall_design: The enriched miRNAs in MSCs-exosome was compared with NIH3T3-exosome as a control

first: Bral

last: Hritu

first: Yoko

last: Yokoyama


title: LncRNA-sequencing of bovine MAC-T cells

status: Public on Aug 06 2021

city: Wuhan

first: Changmin

last: Hu

state: Hubei

address: No.1 Shizishan Street

institute: Huazhong Agricultural University

summary: Escherichia coli and Staphylococcus aureus are two common pathogenic microorganisms that cause mastitis in dairy cows. They can cause clinical mastitis and subclinical mastitis. In recent studies, lncRNAs have been found to play an important role in the immune responses triggered by microbial inducers. However, the actions of lncRNAs in bovine mastitis remain unclear. The purpose of this study was to explore the lncRNA profile on mastitis.

overall_design: LncRNA sequencing for 9 samples. Examining MAC-T cells in 3 conditions (S. aureus treated, E. coli treated, untreated), each with 3 replicates.


title: Transcriptional profiling reveals differential effect of in vivo porcine reproductive and respiratory syndrome virus infection on infected and bystander pulmonary alveolar macrophage cells

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

summary: Porcine reproductive and respiratory syndrome virus (PRRSV) remains a serious threat to the swine industry worldwide for many years. PRRSV has a high tropism for swine pulmonary alveolar macrophages (PAM), an essential innate immune cell. Here, we used RNA-sequencing approach to examine the transcriptional profile of in vivo infected and bystander PAM in the lung of PRRSV-infected swine at 7 days post-infection (dpi). We utilize the PRRSV virion stably expressing EGFP reporter gene to discriminate infected and bystander PAM cells. This work will allow us to differentiate the direct and indirect effect of infection at the cellular level. Firstly, average ~4.2% of reads from infected, while only ~0.06 % reads from bystander cells found mapping to the FL12-EGFP genome. Though most differentially expressed genes (DEGs) are shared between infected and bystander PAM compared to PAM from mock-infected animals, infected cells produce more inflammatory cytokines, interferon signatures, and antiviral immune genes than bystander cells. Importantly, upregulation of NFKB inhibitors (NFKBI) (NFKBIA, NFKBIZ, and TNFAIP3) and T cell exhaustion genes (PD-L1 (CD274), PRDM1, and IL10) was exclusively observed in infected cells. In-situ staining of lung tissue using NFKBI RNA probes confirms temporal upregulation of these immune regulators. Both NFKBI and T-cell exhaustion are prominent immune escape mechanism noted in a several viral infections, however, their role is unexplored in PRRSV pathogenesis. Collectively, these results reveal distinctive transcriptional changes occur within infected and bystander PAM and unique upregulation of NFKBI and T-cell exhaustion pathway in infected PAM indicates a strategy employ by PRRSV to subverts host immune responses.

overall_design: For both control (mock) and infected pigs the transcriptome of the Pulmonary alveolar macrophages (PAM) was sequenced; infected pigs were further divided into a bystander group and a FL12-EFGP+ group. Each group had three biological replicates each.

first: Jayeshbhai

last: Chaudhari

first: Chia

middle: S

last: Liew

middle: M

first: Hiep

middle: L

last: Vu


title: mRNA Sequencing analysis of MED30 deleted mice.

city: la jolla

first: Siting

last: Zhu

state: california

address: 9500 Gilman Drive, University of California San Diego

department: Medicine

institute: UCSD

summary: To study the transcriptome in developing heart controlled by the intact Mediator complex. RNA-seq analysis was performed on RNA extracted from hearts of Med30 cKO and control littermates at E10.5.  From this analysis, 10,637 genes were expressed in both mutant and control cardiomyocytes. Of these, 31 genes were significantly upregulated, and 45 genes were significantly downregulated (log2fold > 1, adjusted p value < 0.05) in mutant cardiomyocyte relative to controls. To identify genes responsible for the rapidly developed phenotype in Med30 icKO mice, we performed RNA-seq analysis of RNA extracted from adult cardiomyocytes isolated from Med30 icKO and control mice at 4-weeks post tamoxifen injection. From this analysis, 9517 genes were detected in both mutant and control cardiomyocytes. Of these, 1153 and 1509 were significantly (log2fold > 1, adjust p value < 0.05) up- or downregulated, respectively, in mutant cardiomyocyte relative to controls

overall_design: Heart mRNA analysis of E10.5 and 4 weeks post-TAM wild type (WT) and MED30f/f,Cre+ mice

first: Yang

middle: E

last: Li

first: Xi

last: Fang


title: Gold nanorod based delivery system could bring about superior therapy effect of Ramucirumab through direct cytotoxicity to cancer cell mediated by differential regulation of phagocytosis in gastric cancer cell

city: Beijing

first: Minzhi

last: Zhao

address: zhongguancunbeiyitiao NO.11

institute: National Center for Nanoscience and Technology of China

summary: Gastric Cancer (GC) is one of the most serious cancers with high incidence and mortality all over the world. Chemotherapy hadn’t led to desirable effect and targeted therapy brings about a new stage to cancer treatment. Ramucirumab is the first FDA-approved monotherapy for advanced gastric cancer. It is well known that gold nanorod, a nontoxic biocompatible nanomaterial, is an especially promising candidate for cancer theranostic. In this study, Ramucirumab (Ab) were first modified by gold nanoparticles to enhance uptake efficiency. The simple Nano-delivery system had taken perfect aggregation effect in vivo even better than 5-fold Ab treatment. Gold nanomaterials, especially gold nanorod (AuNR), could induce direct cytotoxic effect to cancer cell in the presence of Ab, while Ab or gold nanoparticle themselves couldn’t lead to such direct killing effect even at an extremely high concentration. Transcriptomic and proteomic analyses revealed the mechanism of this direct cytotoxicity.

overall_design: GC cells treated with antibody and nanoparticles with two different shapes.

first: Linyang

last: Fan

first: Weizhi

last: Wang


title: RNA-sequence data of mouse liver sinusoidal endothelial cells on day 14 after partial hepatectomy (PHx) or sham operation

city: Xi'an

first: Bai

last: Ruan

state: Shannxi

address: No.169, Changle Road

institute: Fourth Military Medical University

summary: The cellular and molecular mechanisms involved in liver regeneration following partial hepatectomy (PHx) are complicated. Liver sinusoidal endothelial cells (LSECs) play key roles in orchestrating liver regeneration, especially during the inductive phase and angiogenic phase post PHx (from day 0 to day 8). However, the expression profile of LSECs during the late phase of regeneration remains poorly explored. Thus, we purified LSECs from mice underwent PHx or sham operation at day 14 to unravel their transcriptome changes in the late phase of liver regeneration.

overall_design: mRNA profiles of sham or PHx group were generated by RNA sequencing, in triplicate, using Illumina HiSeq 3000.

first: Lin

first: Juanli

last: Duan


title: miR-1-mediated repression of V-ATPase subunits is essential for complex assembly and muscle physiology

city: Vienna

first: Jingkui

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

summary: We report the transcriptomes of muscle cells sorted from C. elegans 1.5-fold embryos with or without the muscle-specific miRNA miR-1

overall_design: 4 QuantSeq libraries from body-wall muscle cells of 1.5 fold C. elegans embryos. 2 replicates for wt and 2 replicates for mir-1(luc108) I. Body-wall muscle cells were sorted based on myo-3p::YFP positive expression (using FACS)

first: Paula

last: Gutiérrez-Pérez

first: Emilio

last: Santillán

first: Thomas

last: Lendl

first: Anna

last: Schrempf

last: Steinacker

first: Mila

last: Asparuhova

first: Marlene

last: Brandstetter

first: David

last: Haselbach

first: Luisa

last: Cochella


title: Whole genome profiling of murine lymphocytes and statistical validation of a panel of immune molecules to predict vaccine efficacy against Mycobacterium tuberculosis

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

summary:
Transcriptional profiling of splenic lymphocytes derived from vaccinated mice, and ex-vivo exposed to M.tb.-infected macrophages in culture.
Splenocytes from mice innoculated with Mycobacterium bovis BCG Pasteur (PAS), or M. bovis BCG Copenhagen (SSI), or heat killed BCG SSI (HK), or uninfected control, were ex vivo co-cultured with mouse bone marrow macrophages previously infected with M. tb.

overall_design: Mouse splenocytes from 3 different immunizations (plus Naive control), after ex-vivo exposure to MtB infected macrophages in co-culture, were re-isolated and RNA extracted for Illumina microarray

first: Sherry

last: Kurtz

first: Paul

last: Gardina

first: Patrik

last: Ryden

first: Karen

last: Elkins


title: EGR1 addiction in diffuse large B cell lymphoma

city: Madison

first: Lixin

last: Rui

state: WI

address: 1111 Highland ave, Room 4053

institute: Wisconsin Ins for Medical Res

summary: Diffuse large B-cell lymphoma (DLBCL) is the most common non-Hodgkin lymphoma, including two main molecular subtypes termed activated B cell-like (ABC) and germinal center B cell-like (GCB). ABC DLBCL is less curable and identification of new molecular targets is needed for the development of effective therapeutic agents. Here, we focused on EGR1, a transcription factor that is regulated by the B cell receptor and JAK1/STAT3 signaling pathway in ABC DLBCL. ChIP-Seq and RNA-Seq analyses revealed that gene regulation by EGR1 in ABC DLBCL accentuates multiple oncogenic pathways, including MYC and E2F, while dampening the lethal type I IFN pathway.

overall_design:
TMD8 and OCI-LY10 cells were treated by shsc4 or shEGR1 knockdown, ChIP-seq experiments were performed by EGR1 antibody (Santa Cruz sc-110).
Cells transduced with control shRNA, shEGR1#8 or shEGR1#9 in OCI-LY10, TMD8 and SUDHL2 cells were induced with 20 ng/ml doxycycline for 2 days. Total RNA from these cells was then used for RNA-seq analysis.

first: Li

last: Lu

first: Shuichi

last: Kimpara


title: Cellular crosstalk regulates the aqueous humor outflow pathway and provides new targets for glaucoma therapies

city: Chicago

first: Benjamin

middle: R

last: Thomson

state: IL

address: 303 E Superior St. SQ8-500

department: Feinberg Cardiovascular and Renal Research Institute

institute: Northwestern University Feinberg School of Medicine

summary: Angiopoietin-1 signaling is essential for development of Schlemm's canal, a large lymphatic-like endothelial vessel in the iridocorneal angle. Single cell RNA sequencing is a powerful tool allowing for examination of the specific transcriptome of each cell type within a tissue. Here, we used single cell RNA sequencing to examin the structures of the mouse iridocorneal angle, using loss of Schlemm's canal in neural-crest specific Angpt1 knockout mice to aid in identification of Schlemm's canal endothelial cells. This dataset provides a resource for analysis of trabecular meshwork / Schlemm's canal crosstalk and the role(s) of Angpt1 in formation of the iridocorneal angle.

overall_design: The 10x Genomics Chromium platform was used to obtain single cell transcriptomes from iridocorneal angle region of 6 week old wild-type and neural crest-specific Angpt1 knockout mice.

first: Pan

last: Liu

first: Tuncer

last: Onay

first: Jing

last: Du

first: Stuart

middle: W

last: Tompson

first: Terri

last: Young

last: Jin

first: Susan

last: Quaggin


title: LncRNA expression profile in hepar tissues of 12h after brain death or matched non-brain death donor liver transplantation

city: Zhengzhou

first: chen

last: sanyang

state: erqi

address: No.1, East Jian She Road

department: Department of Hepatobiliary and Pancreatic Surgery

institute: The First Affiliated Hospital of Zhengzhou University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary:
Brain death donor liver is an important organ source for liver transplantation.The liver injury after brain death donor liver transplantation is serious and the mechanism is unknown.In order to explore the role of lncRNAs and circRNAs expression profile and their biological functions in liver injury after brain death and liver transplantation, lncRNA and mRNA microarray expression profile were tested in the liver after brain death and normal liver transplantation.And this study lays a foundation for future studies on the potential role of lncRNAs in liver injury after brain death donor liver transplantation.

To determine the LncRNA expression profile in hepar tissues of 12h after brain death donor liver transplantation and  matched non-brain death donor liver transplantation, we uesed  LncRNA microArray analysis form Arraystar to examine the expression of LncRNAs and circRNAs  in hepar tissues of 12h after brain death donor liver transplantation and matched non-brain death donor liver transplantation.

overall_design: Hepar tissues from 12h after liver transplantation were distributed into two experimental groups: brain death donor liver transplantation group and  matched non-brain death donor liver transplantation group, then perform LncRNAs chips by Arraystar Rat LncRNAs chip (Arraystar)


title: CD271 is preferentially expressed and essential for cell proliferation in squamous cell carcinoma of the lung

city: Natori, Miyagi

first: Keiichi

last: Tamai

address: 1-47, Nodayama, Shiote, Medeshima

institute: Miyagi Cancer Center

summary: Squamous cell carcinoma is a major type of cancer in the lung. While several therapeutic target molecules for lung adenocarcinoma have been identified, little is known about lung squamous cell carcinoma (LSCC). We recently reported that CD271 (p75 neurotrophin receptor) serves as a marker for tumor initiation and is a key regulator of cell proliferation in hypopharyngeal squamous cell carcinoma. In this study, we found that CD271 was also expressed in squamous cell carcinoma, but not in adenocarcinoma, of several tissues, including the lung. To examine CD271’s role in LSCC, we established xenograft cell lines from LSCC patients. Within the sorted live LSCC cell population, the CD271high cells were primarily cycling through the G2/M phase, while the CD271low cells were mostly in the G0 phase. CD271 knockdown in the LSCC cells completely suppressed their proliferation and tumor-formation capability, and increased their cell-cycle arrest in the G0 phase. In the CD271-knockdown cells, ERK-phosphorylation was decreased, while no change was observed in the IκBα-, p65-, or Akt-phosphorylation. Treatment with the MEK inhibitor U0126 decreased the LSCC cells’ proliferation capability. Microarray analysis revealed that CD271 knockdown attenuated the RAS-related pathways. The knockdown of TrkB, which forms a heterodimer with CD271 and accelerates its downstream signaling, partially inhibited the LSCC cell proliferation. These results indicated that LSCC exclusively depends on CD271 for cell proliferation, in part through ERK-signaling activation.

overall_design: To compare the pathway of CD271 knockdown cells, total RNA obtained from siRNA control MCC148c (human lung squamous cell carcinoma cell line) cells (sicontrol-1 to sicontrol-4, n=4) and CD271 knockdown MCC148c cells (siCD271#1-1, siCD271#1-2, siCD271#2-1 and siCD271#2-2, n=4).

first: Mai

last: Mochizuki

first: Mao

last: Nakamura

first: Rie

last: Sibuya

first: Toshimasa

last: Okazaki

first: Jiro

last: Abe

first: Satomi

last: Takahashi

first: Atsushi

last: Takano

first: Hiroyuki

last: Ito

first: Tomoyuki

last: Yokose

first: Yohei

last: Miyagi

first: Yataro

last: Daigo

first: Ikuro

last: Sato

first: Kennichi

last: Satoh

first: Kazuo

last: Sugamura

first: Kazunori

last: Yamaguchi


title: Investigation of gene expression profiles in CD4+ T cells from SLE patients and normal controls

status: Public on Aug 05 2021

city: Shanghai

first: Xiao

last: Liu

state: Shanghai

address: 12 Middle Wulumuqi Road

institute: Huashan Hospital, Fudan University

summary: To investigate the lncRNAs expression profiling in CD4+ T cells of systemic lupus erythematosus (SLE) patients, we have employed “Agilent Human lncRNA 4*180K microarray” as a discovery platform to identify lncRNAs and mRNAs expression signatures in CD4+ T cells between SLE patients and normal controls. CD4+ T cells were isolated from peripheral blood mononuclear cells (PBMCs) of peripheral blood in SLE patients and normal controls, respectively.

overall_design: Gene expression was measured in CD4+ T cells from peripheral blood of SLE patients and normal controls.

first: Haihong

last: Qin


title: scRNA-seq of P20 mouse cochlea

last: Xue

address: Zhizaoju Road 639

department: Otolaryngology

institute: Shanghai Jiaotong University School of Medicine

summary: ARHL has been thought to result from disordered hair cell function and their loss. ARHL has a significant genetic component. We sought to determine the expression in the cochlea of genes associated with single nucleotide polymorphisms linked to ARHL. We find widespread and varying expression of genes associated with these SNPs in subtypes of cells in the cochlea identified by single-cell RNA sequencing. Genes associated with SNPs with the highest significance were preferentially expressed highly in hair cells while genes associated with SNPs with a lower significance were expressed more universally.

overall_design: Examination of expression patterns of genes expressed in day 20 mouse cochlea.

first: Lei

last: Song

first: Hao

last: Wu

first: Dhasakumar

last: Navaratnam


title: The LiaFSR transcriptome reveals an interconnected regulatory network in group A Streptococcus

city: Houston

first: Anthony

last: Flores

state: TX

address: 6431 Fannin St., MSB 3.130

institute: UTHSC/McGovern Medical School

summary: The mechanisms by which bacteria sense the host environment and alter gene expression are poorly understood.  LiaFSR is a gene regulatory system unique to Gram-positive bacteria including group A Streptococcus (GAS) and responds to cell envelope stress. We previously showed that LiaF acts as an inhibitor to LiaFSR activation in GAS. To better understand gene regulation associated with LiaFSR activation, we performed RNA-sequencing on isogenic deletion mutants fixed in a LiaFSR “always on” (DliaF) or “always off” (DliaR) state. Transcriptome analyses of DliaF and DliaR in GAS showed near perfect inverse correlation including the gene encoding the global transcriptional regulator SpxA2.  In addition, mutant transcriptomes included genes encoding multiple virulence factors and showed substantial overlap with the CovRS regulon. Chromatin immunoprecipitation quantitative PCR demonstrated direct spxA2 gene regulation following activation of the response regulator, LiaR.  High SpxA2 levels as a result of LiaFSR activation were directly correlated with increased CovR-regulated virulence gene transcription.  Further, consistent with known virulence gene repression by phosphorylated CovR, elevated SpxA2 levels were inversely correlated with CovR phosphorylation. Despite increased transcription of several virulence factors, DliaF (high SpxA2) exhibited a paradoxical virulence phenotype in both in vivo mouse and ex vivo human blood models of disease.  Likewise, despite decreased virulence factor transcription in DliaR (low SpxA2), increased virulence was observed in an in vivo mouse model of disease – a phenotype attributable, in part, to known SpxA2-associated speB transcription. Our findings provide evidence of a critical role of LiaFSR in sensing the host environment and suggest a potential mechanism for gene regulatory system crosstalk shared by many Gram-positive pathogens.

overall_design: Comparison of wild-type to mutants lacking the response regulator (LiaR) or the accessory protein (LiaF) of the LiaFSR system in group A Streptococcus

first: Misu

last: Sanson

first: Luis

last: Vega

first: Brittany

last: Shah

first: Shrijana

last: Regmi

first: M

middle: B

last: Cubria

first: Nicola

last: Horstmann

first: Samuel

last: Shelburne III


title: High-throughput sequencing Analysis of mouse BMDM cell Transcriptomes after LPS Challenge

city: Hangzhou

first: Di

last: Wang

state: Zhejiang

address: Yuhgang Tang Rd No.866

department: School of Medicine

institute: Zhejiang University

summary:
Purpose: Mouse BMDM is the universal cell type of studying innate immunity.This study was designed to analyze LPS induced innate immune respone and the gene expression in WT and HDAC3 KO BMDMs.
Methods: BMDM cells from Hdac3f/f  and Lyz2-Cre-Hdac3f/f were treated with or without LPS for 4 hours. Then mRNA profiles of these samles were generated by High-throughput sequencing analysis, in triplicate, using illumina HiSeqTM2000/MiSeq. And the differencial mRNA profiles were analyzed.
Results: mRNA profiles were analyzed, and differencial expression profiles were compared .
Conclusions: Our study demostrated the transcriptional profiles of BMDMs from Hdac3f/f  and Lyz2-Cre-Hdac3f/f mice upon LPS challenge, with biologic replicates, generated by RNA-seq technology.

overall_design: mRNA profiles of BMDM cells from Hdac3f/f  and Lyz2-Cre-Hdac3f/f  mice treated with LPS were generated by High-throughput sequencing, in triplicate, using HiSeqTM2000/MiSeq.

first: Zhexu

last: Chi

first: Sheng

last: Chen

first: Ting

last: Xu


title: The ETS Transcription Factor ERF Controls the Exit from the Embryonic Rosette-stage of Pluripotency.

first: Desiree

last: Tillo

address: 41 Center Dr, Room D310

institute: NIH/NCI

type: Methylation profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Catabolism of strigolactones by a carboxylesterase

first: Yuxin

last: Hu

address: No.20 Nanxincun, Xiangshan

department: Key Laboratory of Plant Molecular Physiology

institute: Institute of Botany, CAS

summary: Strigolactones (SLs) are carotenoid-derived plant hormones that control shoot branching and communications between host plants and symbiotic fungi or root parasitic plants. Extensive studies have identified the key components participating in SL biosynthesis and signaling, whereas the catabolism or deactivation of endogenous SLs in planta remains largely unknown. Here we report that the Arabidopsis carboxylesterase 15 (AtCXE15) and its orthologues function as efficient hydrolases of SLs. We show that overexpression of AtCXE15 promotes shoot branching by dampening SL-inhibited axillary bud outgrowth. We further demonstrate that AtCXE15 could bind and efficiently hydrolyze SLs both in vitro and in planta. We also provide evidence that AtCXE15 is capable to catalyze hydrolysis of diverse SL analogues and that such CXE15-dependent catabolism of SLs is evolutionarily conserved in seed plants. These results disclose a catalytic mechanism underlying homeostatic regulation of SLs in plants, which also provides a rational approach to spatial-temporally manipulate the endogenous SLs and thus architecture of crops and ornamental plants.

overall_design: Transcriptomic profiling of SL-dependent responses using SL signaling mutant atd14-1,  AtCXE15-overexpressing transgenic plant with SL defect phenotype, and Col-0 (WT).

first: Enjun


title: Paraoxonase 2 Deficiency in Mice Alters Motor Behavior and Causes Region-Specific Transcript Changes in the Brain

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Araoxonase 2 (PON2) is an intracellular antioxidant enzyme shown to play an important role in mitigating oxidative stress in the brain. Oxidative stress is a common mechanism of toxicity for neurotoxicants and is increasingly implicated in the etiology of multiple neurological diseases. While PON2 deficiency increases oxidative stress in the brain in-vitro, little is known about its effects on behavior in-vivo and what global transcript changes occur from PON2 deficiency. Therefore, we sought to characterize the effects of PON2 deficiency on behavior in mice, with an emphasis on locomotion, and evaluate transcriptional changes with RNA-Seq. Behavioral endpoints included home-cage behavior (Noldus PhenoTyper), motor coordination (Rotarod) and various gait metrics (Noldus CatWalk). Home-cage behavior analysis showed PON2 deficient mice had increased activity at night compared to wildtype controls and spent more time in the center of the cage, displaying a possible anxiolytic phenotype. PON2 deficient mice had significantly shorter latency to fall when tested on the rotarod, suggesting impaired motor coordination. Minimal gait alterations were observed, with decreased girdle support posture noted as the only significant change with PON2 deficiency. Finally, A subset of samples were utilized for RNA-Seq analysis, looking at three discrete brain regions: cerebral cortex, striatum and cerebellum. Highly regional- and sex-specific changes in RNA expression were found when comparing PON2 deficient and wildtype mice, suggesting PON2 may play distinct regional roles in the brain in a sex-specific manner. Taken together, these findings demonstrates that PON2 deficiency significantly alters the brain on both a biochemical and phenotypic level, with a specific impact on motor function. This data has implications for future gene-environment toxicological studies and warrants further investigation of PON2 in the brain.

overall_design: Male and female wildtype (WT) and PON2 deficient (PON2-def) mice (Ng et al., 2006) on a C57BL/6J background were used for this study. Seven to ten animals were used per sex per group. Mice were bred from PON2 deficient heterozygous crosses with resulting WT and PON2-def homozygous littermates used in rolling cohorts. Behavioral testing began at 3 – 4 months of age. Mice were housed in a specific pathogen-free facility on a 14-hour light/ 10-hour dark cycle with ad libitum access to food and water. All procedures were conducted in accordance with the National Institute of Health Guide for the Use and Care of Laboratory Animals and were approved by the University of Washington Institutional Animal Care and Use Committee. Mice were sacrificed at 3 – 4 months of age upon conclusion of behavioral testing. Cerebral cortex, striatum and cerebellum were fresh dissected (Spijker 2011) and flash frozen in liquid nitrogen. Tissue was pulverized with a pre-chilled mortar and pestle into a fine powder, stored at −80°C and aliquoted into appropriate buffers for downstream testing.

first: Jacqueline

last: Garrick

first: Toby

last: Cole

first: Theo

last: Bammler

first: Judit

last: Marsillach

first: Clement

last: Furlong

first: Lucio

last: Costa


title: Chiltepin pepper RNA-Seq data of two fruit development stages

city: Hermosillo

first: A.

middle: Corina

last: Hayano-Kanashiro

state: Sonora

address: Avenida Luis Donaldo Colosio s/n Edificio 7G, Colonia Centro

department: Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora

country: Mexico

institute: Universidad de Sonora

summary: Two fruit development stages of the wild chiltepin pepper (Capsicum annuum var. glabriusculum) were studied. RNA-Seq data was obtained from fruits at 20 and 68 days after anthesis with two biological replicates for a total of 4 samples. 260 million raw reads were sequenced and over 80% of them mapped back to the Capsicum annuum genome.

overall_design: Single design (1 factor) with two levels (time of fruit development): 20 and 68 days after anthesis, and two replicates per factor level.

first: A

middle: C

first: Octavio

last: Martínez-de la Vega

first: Fernando

last: Razo-Mendivil

last: Hernández-Godínez


title: eccDNA biogenesis and its role in innate immunity

city: Boston

first: Yi

last: Zhang

state: MA

address: 200 Longwood Avenue WAB 149

department: PCMM

institute: Boston Children's Hospital / Harvard Medical School

summary: Extrachromosomal circular DNA elements (EccDNAs) have been described in the literature for several decades and are known for their wide existence across species as well as their high heterogeneity in genomic origins. Due to their scarcity and lack of validation tools, their biogenesis as well as their functions are largely unknown. Here, by using a newly developed circular DNA enrichment method, we purified eccDNAs from different cells and mapped their genomic location using both Illumine and Nanopore sequencing. We found that eccDNAs are mapped to genome in a largely random fashion, suggesting a biogenesis mechanism of random ligation of genomic DNA fragments. Consistently, we found that apoptosis inducers can increase the eccDNA generation, which is dependent on DNase 1/3 and DNA ligase 3. Importantly, we demonstrate that eccDNAs function as potent innate immunostimulants in a sequence-independent, but circularization-dependent fashion.

overall_design: We developed a new three-step eccDNA enrichment method that allows the purification of eccDNA. We used eccDNAs purified from mESCs because the genetic integrity of ESCs is believed to be maintained during culture. To get the full-length sequence of eccDNA, we employed rolling-circle amplification of the purified eccDNA followed by Oxford Nanopore single-molecular long read sequencing. In addition, we sequenced the purified eccDNA from mESCs using Tn5 transposase tagmentation followed by Illumina paired-end sequencing, without rolling-circle amplification.

first: Yuangao

last: Wang

first: Meng

first: Mohamed

middle: N

last: Djekidel

first: Huan

first: Di

last: Liu

first: Fred

last: Alt


title: Expression data from neuroblastoma cells treated with MI-773

city: Suzhou

first: Zimu

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

summary: Neuroblastoma (NB) is a common pediatric malignancy tumor with poor outcome. Recent studies show that MDM2 protein inhibitors are promising anti-cancer agents. MI-773 is a novel and specific antagonist of MDM2 and the molecular mechanisms of MI-773 in neuroblastoma are still unclear. In this study, we used microarrays to analyze the global change in gene expression as a result of MI-773 treatment in the human neuroblastoma cell line SH-SY5Y.

overall_design: We treated SH-SY5Y cells with the MI-773 (1 uM) for 24 h and then extracted the global RNA. We subjected the RNA to Arraystar Human LncRNA microarray V4.

first: Zhi-Heng

last: Li

first: Jian

last: Pan


title: Hypoxia induces trophoblast migration and invasion gene pathways, a subset of which are reduced in preeclampsia

city: Newark

first: Nataki

middle: C.

last: Douglas

state: NJ

address: 185 S Orange Ave, MBS E569

department: Ob-Gyn and Women's Health

institute: Rutgers-New Jersey Medical School

summary: Placentation requires the proper regulation of extravillous trophoblast (EVT) migration and invasion into the decidua and maternal vasculature, processes which are initiated in physiologic hypoxic conditions. Abnormal EVT migration and/or invasion have been suggested to lead to pregnancy complications, such as preeclampsia. The objectives of this study are to determine how exposure to hypoxia impacts gene expression and cellular motility of first trimester trophoblasts, and to assess if expression of migration-associated genes is dysregulated in 2nd trimester chorionic villous samples (CVS) from preeclampsia pregnancies relative to CVS from healthy pregnancies.  The 1st trimester trophoblast cell line, HTR8/SVneo, was used to investigate the relationship between hypoxia and Notch signaling in trophoblast migration and invasion. RNA sequencing and quantitative RT-PCR analyses show that exposure to hypoxia (2.5% O2) activates Notch signaling in HTR-8/SVneo. We demonstrate that exposure of HTR-8/SVneo to hypoxia induces expression of genes associated with cellular migration and invasion and increases HTR-8/SVneo cellular migration and invasion, whereas inhibition of gamma-secretase decreases Notch signaling and decreases HTR-8/SVneo migration and invasion.   Analysis of RNA sequencing data from CVS of preeclampsia and uncomplicated pregnancies identified significant differentially expressed genes that are involved in cellular migration and invasion. Decreased expression of migration and invasion genes in CVS from preeclampsia pregnancies, may impair trophoblast migration and invasion in the 2nd trimester of pregnancy, resulting in the development of preeclampsia.

overall_design: 1) HTR-8/SVneo: 6 samples were analyzed; n=3 samples for the control group (FC1, FC2, FC3) were exposed to normoxic conditions (21% 02); n=3 samples for the experimental group (Hyp7, Hyp8, Hyp9) were exposed to hypoxic conditions (2.5% 02).  For each condition, RNA was extracted from cells that were grown and processed independently to serve a replicates.    2) Chorionic villous sampling: n=6 samples from 6 unique human pregnancies were analyzed; n=4 samples were from uncomplicated, healthy pregnancies (CVS24, CVS25, CVS27, CVS33); n=2 samples were from preeclampsia pregnancies (CVS20, CVS32)

first: Barry

last: Perlman

first: Audrey

middle: A

last: Merriam

first: Alexander

last: Lemenze

first: Salma

last: Begum


title: Regions of open chromatin in naive CD21low and CD21pos B cells from CVID patients and in naive CD21pos B cells from healthy controls

city: Freiburg

first: Baerbel

last: Keller

department: Department of Rheumatology and clinical immunology

country: Germany

institute: University Medical Center Freiburg

summary: ATAC seq data from CVID-derived naive CD21low B cells were compared to naive CD21pos Bcells from patients and healthy controls. The data revealed a distinct enahncer landscape in CD21low B cells.

overall_design: B cell populations were sorted from peripheral blood and processed for ATACseq

first: B

first: K

last: Warnatz

first: C

last: Bossen


title: CLAMP and Zelda function together as pioneer transcription factors to promote Drosophila zygotic genome activation

city: Ithaca

first: Ellie

last: Duan

state: New York

address: 507 Tower Rd., Ithaca, NY 14853, Ithaca, NY 1485

department: Animal Science

institute: Cornell University


title: Cardiac Myoediting Attenuates Cardiac Abnormalities in Human and Mouse Models of Duchenne Muscular Dystrophy

city: New York

first: Zhaoning

address: 701 West 168th Street Hammer 14 - 1410

department: Genetics and Development

institute: Columbia University

summary: Rationale – Absence of the dystrophin gene in Duchenne muscular dystrophy (DMD) results in the degeneration of skeletal and cardiac muscles. Owing to advances in respiratory medicine, cardiomyopathy has become a significant aspect of the disease. While CRISPR/Cas9 genome editing technology holds great potential as a novel therapeutic avenue for DMD, little is known about the efficacy of correction of DMD using the CRISPR/Cas9 system in mitigating the cardiomyopathy phenotype in DMD.  Objective – To define the effects of CRISPR/Cas9 genome editing on structural, functional and transcriptional dysregulation in DMD-associated cardiomyopathy.  Methods and Results – We generated induced pluripotent stem cells (iPSCs) from a patient with a deletion of exon 44 of the DMD gene (ΔEx44) and his healthy brother. Here, we targeted exon 45 of the DMD gene by CRISPR/Cas9 genome editing to generate corrected DMD (cDMD) iPSC lines, wherein the DMD open reading frame was restored via reframing (RF) or exon skipping (ES). While DMD cardiomyocytes (CMs) demonstrated morphologic, structural and functional deficits compared to control CMs, CMs from both cDMD lines were similar to control CMs. Bulk RNA-sequencing of DMD CMs showed transcriptional dysregulation consistent with dilated cardiomyopathy, which was mitigated in cDMD CMs. We then corrected DMD CMs by adenoviral delivery of Cas9/gRNA and showed that postnatal correction of DMD CMs reduces their arrhythmogenic potential. Single-nucleus RNA-sequencing of hearts showed reduced transcriptional dysregulation in CMs and fibroblasts in corrected mice compared with DMD mice, consistent with reduced histopathologic changes.  Conclusions – We show that CRISPR/Cas9-mediated correction of DMD ΔEx44 mitigates structural, functional and transcriptional dysregulation consistent with dilated cardiomyopathy irrespective of how the protein reading frame is restored. We show that these effects extend to postnatal editing in iPSC-CMs and mice. These findings provide key insights into the utility of genome editing as a novel therapeutic for DMD-associated cardiomyopathy.

overall_design: DMD ∆Ex44 induced pluripotent stem cells (iPSCs) were corrected by reframing (RF) or exon skipping (ES) of exon 45 using CRISPR/Cas9. RNA was isolated from cardiomyocytes derived from DMD ∆Ex44 and both corrected DMD lines in triplicate for stranded mRNA-Seq.

first: Ayhan

last: Atmanli

first: Eric

last: Olson


title: The endothelial landscape and its role in von Hippel-Lindau disease

status: Public on Aug 04 2021

city: Tübingen

first: Omelyan

last: Trompak

state: BW

address: Otfried-Müller-Straße 14

department: Internal Medicine VIII

institute: University Hospital of Tübingen

summary: We report transcriptome analysis (RNAseq) of VHL-derived BOECs, further supported by in vitro assays, shows that these cells are in disadvantage, as evidenced by loss of cell adhesion capacity, angiogenesis defects, as well as an immune response and oxidative metabolic gene downregulation, that induces oxidative stress. These results would suggest that the endothelium of VHL patients is functionally compromised and more susceptible to tumor development. These findings contribute to shedding light on the vascular landscape of VHL patients preceding the second hit mutation in VHL gene.

overall_design:
Expression level comparison between transcriptomes of blood outgrowth endothelial cells (BOEC) derived from 5 patients harbouring VHL mutations in comparison with 2 control patients.
Control samples are depicted as C# and VHL-harbouring mutation samples are V#, where # is the number.

first: Isabel

last: de Rojas-P

first: Virginia

last: Albiñana

first: Lyudmyla

last: Taranets

first: Lucía

last: Recio-Poveda

first: Angel

last: Cuesta

first: Thales

last: Kronenberger

first: Luisa

last: Botella


title: The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation [PAS-seq]

city: Stanford

first: Daniel

middle: Sunwook

last: Kim

state: CA

address: 269 Campus Drive, CCSR 2150

institute: Stanford School of Medicine

summary: A deep-learning framework interprets multi-omic data across epidermal differentiation, identifying cooperative DNA sequence rules that regulate gene modules. Massively parallel reporter analysis validates temporal dynamics and cis-regulatory logic.

overall_design: PAS-seq performed on days 0-6 of keratinocyte differentiation, every 12 hours (https://www.encodeproject.org/treatment-time-series/ENCSR057HZF/).

first: James

last: Chappell


title: The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation

sample_organism:
Escherichia coli
Homo sapiens

platform_organism:
Escherichia coli
Homo sapiens


title: Estrogen Drives Melanocortin Signaling to Increase Spontaneous Activity

city: San Francisco

first: Holly

last: Ingraham

address: 1550 4th Street, 284F

department: Cellular and Molecular Pharmacology

institute: University of California, San Francisco

summary: Transcriptional profilig of estradiol sensitive genes in the VMHvl of female mice

overall_design:
For the vehicle treatment condtion, 3 biological replicates were analyzed. In the estradiol benzoated (EB) treated group, 4 biological replicates were analyzed. In both cases, each biological replicate represents material isolated from a single mouse.
Please note that the mice are on a mixed background (as they are originally derived from the floxed Esr1 line generated in Sohaib Khan's lab, PMID: 17785410, and therefore come from a 129/Sv lineage).

first: William

last: Krause


title: The fibrosis-targeted collagen/integrins gene profile predicts risk of metastasis in pulmonary neuroendocrine neoplasms

city: Sao Paulo

first: Tabatha

middle: Gutierrez

last: Prieto

state: Sao Paulo

address: Av Dr Arnaldo 455, room 1143

department: Pathology

country: Brazil

institute: Faculty of Medicine of University of Sao Paulo

summary: In this study, we sought to identify differentially expressed collagen/integrin genes in PNENs in order to understand the molecular mechanisms underlying the development of stroma-associated fibrosis for invasion and metastasis. We compared collagen/integrin gene expression profiling between PNE tumors (PNETs) and PNE carcinomas (PNECs) using a two-stage design. First, we used PCR Array System for 84 ECM-related genes, and among them, we found COL1A2, COL3A1, COL5A2, ITGA5, ITGAV, and ITGB1 functionally involved in the formation of the stroma-associated fibrosis among PNENs histological subtypes. Second, we examined the clinical association between the six collagen/integrin genes in tumor tissues from 24 patients with surgically excised PNENs.However, the pathological exam of their resected tissues demonstrated that 10 developed lymph node metastasis and 7 distant metastasis. We demonstrated and validated up regulation of the six fibrogenic genes in PNECs and down regulation in PNETs that were significantly associated with metastasis-free and overall survival (P<0.05). Our study implicates up regulation of fibrogenic genes as a critical molecular event leading to lymph node and distant metastasis in PNENs.

overall_design: The neoplastic area was micro dissected during the frozen section procedure to ensure the inclusion of neoplastic tissue and distant non-neoplastic tissue as control. Total mRNA was extracted from 24 fresh-frozen tumor and normal tissues using the QIAsymphony miRNA CT 400 kit (Qiagen, CA, USA) according to the manufacturer’s instructions. RNA integrity and quality were determined using the Bioanalyzer 2100 (Agilent Technologies). Complementary DNA was synthesized using the c-DNA – RT² First Strand Kit (Qiagen Sample & Assay Technologies) according to the manufacturer’s protocol. The difference of expression in EMT genes was evaluated by the real-time PCR method. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was performed using the RT² Profiler PCR Array System (PAHS-090Z; Qiagen, Dusseldorf, Germany) kit for the human epithelial-to-mesenchymal transition (EMT) pathway with 84 target genes.

first: Juliana

last: Machado-Rugolo

first: Camila

last: Baldavira

first: Ana

middle: P

last: Velosa

first: Walcy

last: Teodoro

first: Alexandre

last: Ab' Saber

first: Vera

last: Capelozzi


title: Effects of Paramylon Extracted from Euglena gracilis EOD-1 on lipid metabolism in the Ileum and Liver in Diet-Induced Obese Mice Analyzed by DNA Microarray.

city: Chiyoda-ku

first: Kento

last: Mio

state: Tokyo

address: 12 Sanban-cho

department: Studies in Human Life Sciences

institute: Otsuma Womenʼs University

summary: We have previously shown that paramylon (PM) supplementation to a high fat diet reduces the postprandial glucose rise, serum total and LDL-cholesterol, and abdominal fat accumulation in mice; however, the mechanism has not been determined. We evaluated the potential mechanism in male C57BL/6J mice fed a high-fat diet supplemented with 5% PM powder, extracted from Eu-glena gracilis, for 12 weeks. Abdominal fat weight, and serum lipids were measured; ileal and hepatic mRNA expression were assessed using DNA microarray and real-time PCR. The poten-tial mechanism of PM on modulating lipid metabolism was explored by gene ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Dietary supplementation with PM resulted in decreased abdominal fat accumulation and serum LDL-cholesterol concentrations via suppression of the digestion and absorption pathway in the ileum and activation of the hepatic PPAR signaling pathway. Improvement in glucose tolerance may be the result of lipid metabolism modification because the glucose metabolism pathway was not detected by GO classification and KEGG pathway analysis. PM intake also directly enhanced immunoglobulin production.

overall_design: High-fat model mice were fed paramylon or control diet (cellulose) for 12 weeks, and ileum and liver were collected after dissection. Total RNA in each organs were extracted by using protocol of RNeasy Mini kit. The resultant single-strand cDNA was fragmented and labeled with biotin. cDNA were hybridized to the GeneArray Mouse 2.0ST Array. The arrays were washed, stained and scanned using the Affymetrix 450 Fluidics Station and GeneChip Scanner 3000 7G according to the manufacturer’s recommendations. The arrays were washed, stained and scanned using the Affymetrix 450 Fluidics Station and GeneChip Scanner 3000 7G according to the manufacturer’s recommendations.

first: Seiichiro

last: Aoe


title: Quantitative Analysis of Wild Type and the newly generated CRISPR/Cas9 Hpn-/- mouse mammary gland gene expression analysis

city: Helsinki

first: Juho

last: Väänänen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary: Transforming growth factor beta (TGFβ) is a multifunctional cytokine with a well-established role in mammary gland development and both oncogenic and tumor-suppressive functions. The extracellular matrix (ECM) indirectly regulates TGFβ activity by acting as a storage compartment of latent TGFβ, but how TGFβ is released from the ECM via proteolytic mechanisms remains largely unknown. In this study, we demonstrate that hepsin, a type II transmembrane protease overexpressed in 70% of breast tumors, promotes canonical TGFβ signaling through the release of latent TGFβ from the ECM-storage compartment. Mammary glands in hepsin CRISPR knock-out mice showed reduced TGFβ signaling and increased epithelial branching, accompanied by increased levels of fibronectin and latent TGFβ1, while overexpression of hepsin in mammary tumors increased TGFβ signaling. Cell-free and cell-based experiments showed that hepsin is capable of direct proteolytic cleavage of fibronectin but not latent TGFβ and, importantly, that the ability of hepsin to activate TGFβ signaling is dependent on fibronectin. Altogether, this study demonstrates a role for hepsin as a regulator of the TGFβ pathway in the mammary gland via a novel mechanism involving proteolytic downmodulation of fibronectin.

overall_design: RNA was extracted from 2-6 weeks old wild-type (N=3, refference samples) and Hpn-/- (N=3) virgin female mammary glands and sequenced with Illumina NextSeq500  (Illumina, San Diego, CA, USA) to quantitate transcriptional changes in gene expression. Pathway and statistical enrichment analysis were performed in GSEA 4.0.3 software (Subramanian et al., 2005 PMID: 16199517).

first: Juha

last: Klefström

first: Denis

last: Belitškin


title: The whole transcriptome RNA sequencing of tumor tissue samples from 61 pancreatic ductal adenocarcinoma patients.

status: Public on Aug 03 2021

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

institute: Fudan University

summary: Tissue samples were collected from 61 stage I/II PDAC cases then were placed into 10% neutral buffered formalin solution, fixed at roomtemperature (8–72 h) and processed routinely into a paraffin embedded tissue block (FFPE). The RNAstorm™ Kit (biotium, USA) was used to extracted and isolated total RNA fraction from FFPE Tissue Samples. RNA libraries were prepared for sequencing using prepared SMARTer® Stranded Total RNA-Seq Kit - Pico Input Mammalian Kit. RNA-seq was performed  by the Illumina sequencing platform on a 150-bp paired-end run.

overall_design: The RNA expression profiles of formalin-fixed, paraffin-embedded PDAC tissue samples by whole transcriptome sequencing.

first: Peng

last: Wang


title: Single-cell RNA sequencing data from hiPSC disease modeling of Loeys-Dietz Syndrome (LDS)

city: Ann Arbor

first: Dogukan

last: Mizrak

state: MI

address: NCRC Building 26, 263S

department: Cardiac Surgery

institute: University of Michigan

summary: For in vitro disease modeling of LDS, we used healthy donor cells (TGFBR1+/+), and generated heterozygote (TGFBR1A230T/+), and homozygote (TGFBR1A230T/A230T) knock-in clones using CRISPR-Cas9 gene editing. We also generated hiPSC from peripheral blood mononuclear cells harvested from an LDS patient, and corrected the mutation in the patient-derived hiPSC. To address the lineage-specific effects of TGFBR1A230T, and SMAD3c.652delA/+, hiPSC were differentiated into cardiovascular progenitor cell-derived smooth muscle cells (CPC-SMC), and neural crest stem cell-derived smooth muscle cells (NCSC-SMC) using in vitro differentiation protocols. We performed large-scale single cell profiling of the resulting CPC-SMC and NCSC-SMC.

overall_design: Using an automated microwell array platform and mRNA capture beads, we generated single-cell RNA-seq profiles of cultured CPC-SMC and NCSC-SMC derived from hiPSC.

first: Bo

last: Yang


title: Development of gene expression signatures for psoriasis

city: Jinan

first: chen

last: cheng

address: 07 Wenhua xi road, Jinan, Shandong

institute: Qilu hospital Shandong University

summary: To further explore the gene expression signatures in psoriatic, we have employed whole genome microarray expression profiling as a discovery platform to identify the potential genes that play a role in the pathogenesis of psoriasis. 3 psoriasis specimens were collected from patients with psoriasis and 3 normal skin were obtained from cosmetic surgeries as controls.The analysis identified a set of 4956 differentially expressed circRNAs，2194 significantly dysregulated lncRNAs，and 1725 discrepant mRNAs .Among all the differential expressed circRNAs, 3016 upregulated circRNAs and 1940 downregulated circRNAs were found in psoriatic lesions compared with normal healthy skin tissues.

first: Meng

last: Qiao

first: Qing

last: Sun


title: The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation [ChIP-seq]

first: Daniel

last: Kim

relation:
Reanalysis of: GSM5330873
Reanalysis of: GSM5330872
Reanalysis of: GSM5330806
Reanalysis of: GSM5330805
Reanalysis of: GSM5330731
Reanalysis of: GSM5330730
Reanalysis of: GSM5330638
Reanalysis of: GSM5330637
Reanalysis of: GSM5331023
Reanalysis of: GSM5331022
Reanalysis of: GSM5331097
Reanalysis of: GSM5331096
Reanalysis of: GSM5331253
Reanalysis of: GSM5331252
Reanalysis of: GSM5331116
Reanalysis of: GSM5331117
Reanalysis of: GSM5330922
Reanalysis of: GSM5330923
SubSeries of: GSE181416

middle: S

first: Adam

last: Rubin

first: Minyi

last: Shi


title: Identify gene expression alterations induced by F-PRT versus S-PRT in a mouse sarcoma model

city: Athens

first: Evdokia

last: Karagouni

state: Attica

address: 127 Vas. Sofias Avenue

department: Department of Microbiology

country: Greece

institute: Hellenic Pasteur Institute

summary: To delineate gene expression changes induced by F-PRT versus S-PRT, we performed transcriptional profiling (RNA-Seq) in skin and bone tissues from a mouse sarcoma model. Differential expression analysis followed by pathway enrichment analysis revealed numerous upregulated pathways by S-PRT, yet unaltered by F-PRT.

overall_design: Mouse skin and bone tissues were harvested and submitted for RNA-Seq

first: Anastasia

last: Velalopoulou

first: Ilias

middle: V

last: Karagounis

first: Gwendolyn

middle: M

last: Cramer

first: Michele

first: Giorgos

last: Skoufos

first: Constantinos

last: Koumenis

first: Keith

last: Cengel

first: Amit

last: Maity

first: Theresa

last: Busch


title: Systemic persistent RNA virus infection is short-lived at the single cell level

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: We report that cells infected with the prototypic arenavirus LCMV are continiously cleared from the infection in a non-cytolytic manner. Non-cytolytic clearance of murine hepatocytes goes along with profound alterations in gene expression.

overall_design: We sorted hepatocytes from 14 week-old Cre-reporting mice (STOP_flox_RFP), which had been neonatally infected with Cre-encoding LCMV according to RFP expression (RFP-positive and RFP-negative). Total cellular RNA of each population was subject to bulk RNAseq. RFP-negative hepatocytes from naive STOP_flox_RFP mice and RFP-positive hepatocytes from naive mice expressing RFP under a liver-specific promoter (STOP_flox_RFP x Alb-Cre) served as controls

first: Peter

last: Reuther

first: Katrin

last: Martin

first: Florian

last: Geier

middle: D

last: Pinschewer


title: TRAP-seq of NTS/AP Calcr neurons

first: Martin

middle: G

last: Myers Jr

address: 1000 Wall St

summary: To identify transcripts enriched in hindbrain Calcr neurons, we employed translated ribosome affinity purification combined with RNA-seq (TRAP-seq).

overall_design: Calcr-Cre mice were either crossed to a R26 Cre-dependent EGFP:L10a mouse line or injected with a Cre-dependent AAV expressing EGFP:L10a in the nucleus of the solitary tract and area postrema (NTS/AP). Ribosome-associated (Bead) and supernatant (Sup) polyA RNA were then isolated for library construction and sequencing.

last: Myers

first: Alan

last: Rupp

first: Wenwen

last: Cheng


title: Arabidopsis CFM6, a CRM domain protein, is involved in the splicing of mitochondrial group II intron 4 of nad5 and normal plant growth

city: Taipei

first: Wan-Hsing

state: Taiwan

address: 128 Academia Road, Section 2, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

summary: CFM6 Knockout mutant affects respiratory complex I biogenesis, which results in mitochondria dysfunction. To better understand the function of CFM6 and to further investigate other possible factors that might result in mutant phenotypes, whole-transcriptome analysis was carried out using RNA-seq from Col-0 and cfm6-1 plants.

overall_design: mRNA profiles of 2-wk-old Col-0 and cfm6-1 were generated by RNA-seq method, with 3 biological replicates, using Illumina HiSeqTM 2500.

first: Wei-Chih

last: Lin


title: Rbfox contributes to a conservative program of self-antigen splicing in thymic epithelial cells

city: Oxford

first: Stephen

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

institute: Kennedy Institute of Rheumatology

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Pten and Dicer1 loss in the mouse uterus causes poorly-differentiated endometrial adenocarcinoma

city: Indianapolis

first: Shannon

last: Hawkins

state: Indiana

institute: Indiana University School of Medicine

summary: Endometrial cancer remains the most common gynecological malignancy in the United States. While the loss of the tumor suppressor, PTEN, is well studied in endometrial cancer, recent studies suggest that DICER1, the endoribonuclease responsible for miRNA genesis, also plays a significant role in endometrial adenocarcinoma. To examine the effects of DICER1 deletion on mRNA and miRNA expression in endometrial cancer, poly-A RNA sequencing (RNA-seq) and small RNA sequencing were performed. Our findings indicate a relationship between appropriate miRNA expression and molecular signaling pathways in the development of poorly-differentiated endometrial adenocarcinoma.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Poly-a RNA and small RNA sequencing on mouse uteri and ishikawa cells.

first: Xiyin

last: Wang

first: Jillian

middle: R

last: Wendel

first: Robert

middle: E

last: Emerson

first: Russell

last: Broaddus

first: Char

middle: J

last: Creighton

first: Douglas

last: Rusch

first: Aaron

last: Buechlein

first: Francesco

last: DeMayo

first: John

last: Lydon


title: Comparative study of gene expression in Aspergillus niger solid and submerged growth during sugar beet pulp utilization

city: Utrecht

first: Ronald

last: de vries

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: westerdijkinstitute

type:
Expression profiling by array
Third-party reanalysis

summary: In this study, we compared the gene expression pattern of A. niger grown in liquid sugar beet pulp (SBP) at different time points, a by-product of the sugar industry that consists mainly of cellulose, xyloglucan, and pectin. Finally, we compared A. niger  genetic response to liquid SBP to that of the same fungus when grown on solid SBP plates and polygalacturonic acid (PGA).

overall_design: In this study, we aimed to reveal the extent to which A. niger response is comparable when grown on solid and submerged cultures. For this, we first studied the gene expression pattern of A. niger grown in liquid sugar beet pulp (SBP) at different time points, a by-product of the sugar industry that consists mainly of cellulose, xyloglucan, and pectin. Finally, we compared A. niger  genetic response to liquid SBP to that of the same fungus when grown on PGA and solid SBP plates (previously deposited with GEO accession GSE66641). Part of PGA and liquid SBP datasets were previously deposited with GEO accession GSE98572 (with Sample ID GSM2600976, GSM2600977,GSM2600984, GSM2600985).

first: Sandra

last: Garrigues

first: Roland

last: Kun

first: Mao

last: Peng

first: Miia

last: Mäkelä

last: de Vries


title: Heterogeneity in the transcriptional response of the human pathogen Aspergillus fumigatus to the antifungal agent caspofungin

status: Public on Aug 02 2021

city: Ribeirao Preto

first: Gustavo

middle: Henrique

last: Goldman

address: Avenida do Cafe

institute: Sao Paulo University

summary: The transcription factor CrzA influences cell wall organization in the pathogenic fungus Aspergillus fumigatus, and also binds to the promoter regions of chitin synthase genes upon exposure to the antifungal drug caspofungin. To gain an overview of the genes directly regulated by CrzA, the CrzA binding sites were determined genome-wide by ChIP-seq

overall_design: The CrzA-tagged strain was grown for 16 hours at 37oC  in minimum liquid media at 220 rpm and then added with 2 ug/ml of caspofungin  for 1 hour minutes (37oC 220 rpm). After crosslinking, the cells were washed and frozen for chromatin extraction and immunoprecipitation.

first: Ana

last: Colabardini

first: Fang

first: Zhiqiang

last: Dong

first: Lakhansing

last: Pardeshi

first: Marina

last: Campos Rocha

first: Jonas

middle: H

last: Costa

first: Thaila

last: Fernanda dos Reis

first: Alec

last: Brown

first: Micha

last: Fridman

first: Taicia

last: Fill

first: Antonis

last: Rokas

first: Iran

last: Malavazi

first: Koon

last: Wong


title: Rbfox contributes to a conservative program of self-antigen splicing in thymic epithelial cells [Rbfox_SKO_RNAseq]

first: Stephen

last: Sansom

summary: Thymic epithelial cells (TEC) guide selection of a T-cell repertoire that is reactive to pathogens but tolerant to self. While this process is known to involve the promiscuous expression of virtually the entire protein-coding gene repertoire by TEC, the extent to which these cells reproduce peripheral isoform structures is unknown. We performed a transcriptomic investigation of transcript structures and splicing factor expression in medullary TEC and 21 peripheral tissues. Our results indicate that TEC re-use a small number of peripheral splicing factors to recreate a limited subset of the peripheral splice isoform repertoire. We found, for example, that TEC lacked both neuronal microexons and the splicing factor, Srrm4, which promotes their inclusion. We demonstrate a functional role for the Rbfox splicing factors in promoting medullary TEC development and the alternative splicing of promiscuously expressed genes. Our findings have implications for understanding autoimmune diseases and the development of antigen-specific immunotherapies.

overall_design: Two biological replicates of two murine mTEC populations were FACS sorted from Rbfox1 and Rbfox2 thymus specific (conditional) knockout mice and littermate controls.

first: Kathrin

last: Jansen

first: Georg

last: Hollander


title: Total RNAseq of fixed M-MDSC isolated from tumor bearing and LCMV infected mice

city: Cambridge

first: Gozde

last: Kar

address: Cambridge

institute: AstraZeneca

summary: Myeloid-derived suppressor cells (MDSC) are major negative regulators of immune responses in cancer and chronic infections. It remains unclear if regulation of MDSC activity at different conditions is controlled by similar mechanisms. In order to compare MDSC in mice with cancer and lymphocytic choriomeningitis virus (LCMV) infection, we would like to perform gene profiling and comparison of M-MDSCs in tumor bearing and LCMV infected mice using total RNAseq:

overall_design: Sort and fix M-MDSC isolated from spleen in 1) naïve mice, 2) LLC tumor bearing mice on 3 weeks, and 3) LCMV infected mice on 2 weeks, 2. extract RNA using a FFPE isolation ki (QIAGEN) with Rnase, 3. Run total RNAseq, 4. Analyze data and compare gene expression between LLC and LCMV mice.

first: Shino

last: Hanabuchi

first: Fernanda

last: Pilataxi

first: Susana

last: Hayes


title: Rbfox contributes to a conservative program of self-antigen splicing in thymic epithelial cells [mTEC_ONT_RNAseq]

overall_design: Three biological replicates samples of two wildtype murine mTEC populations were FACS sorted and subjected to Oxford Nanopore Technology long-read sequencing.


title: Integrative genome-wide analysis of dopaminergic neuron-specific PARIS expression dissects recognition of multiple PPAR-γ associated gene regulation (ChIP-Seq).

city: Ulm

first: Karin

last: Danzer

state: Baden-Wurttemberg

address: University of Ulm Campus, Building N24, R3306 Albert-Einstein-Allee 11

department: Department of Neurology

institute: University of Ulm / DZNE, Ulm

summary: PURPOSE: The transcriptional repressor PARIS (ZNF746) was initially identified as a pathogenic co-substrate of PINK1 and parkin that leads to Parkinson’s disease (PD) by disrupting mitochondrial biogenesis through PPARγ coactivator -1α (PGC-1α) suppression. Later, accumulation of PARIS in dopamine (DA) neurons that cause neurotoxicity has been studied widely and growing evidence has linked defective mitochondrial biogenesis to PD pathogenesis. Yet, the mechanistic underpinnings of this link remain elusive. METHODS: We performed a global, model-based analysis of PARIS genomic occupancy using chromatin immune-precipitation followed by sequencing (ChIP-seq) on SHSY-5Y in human cell line. The dataset is composed of PARIS and control samples, each with one replicate only. For each sample, after quality control as mentioned above, reads were separately aligned to the latest human genome (NCBI; GRCh38) using Bowtie with the parameter “-m 1” to retain uniquely mapped reads only. The R packages ChIPQC v1.20.0 and PhantomPeakQualTools v1.2.2 were used to confirm the quality of the aligned bam files based on the ChIP-seq guidelines by ENCODE consortium (NSC >= 1.05; RSC >= 0.8, Qtag={-2,-1,0,1,2}). QC-confirmed bam files were subject to differential peak calling using MACS v1.4.220 with the following parameters: -t Sample.sam -c Control.sam --format SAM -g hs -B -S --call-subpeaks. Peak annotation and visualization were done using the R packages ChIPseeker v1.20.0 and clusterProfiler v3.12.0, respectively. RESULTS: We showed that PPARγ acts as a master regulator of transcriptomic changes induced by PARIS in the clusters of Drosophila dopaminergic neurons. Also, we revealed that PARIS directly modulates expression of PPARγ target genes by physically binding to the promoter regions. And finally, we observed a PARIS binding motif at the promoter proximal site of PPARγ, implying a direct regulatory effect of PARIS on PPARγ expression profile. CONCLUSION: PARIS displays adverse effects on modulation of PPARγ associated gene clusters. Our work revealed a pivotal role of PPARγ in PARIS-driven neurodegeneration.

overall_design: Examination of PARIS binding sites in neuroblastoma (SHSY-5Y) cell line.

first: Sung

middle: U

last: Kang

first: Volkan

last: Yazar


title: Illumina Infinium MethylationEPIC BeadChip (850k) data of NCCIT / 2102EP cells deficient for CD24 and parental controls

status: Public on Aug 01 2021

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Moorenstr. 5

department: Dep. of Urology

institute: Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University

type: Methylation profiling by genome tiling array

summary: Illumina Infinium MethylationEPIC BeadChip (850k) array analysis of DNA methylation of embryonal carcinoma cell lines NCCIT and 2102EP deficient for CD24 and parental cells. CD24 deficiency was genereted by CRISPR/Cas9 method. Three different NCCIT and 2102EP knock out clones were analyzed.

overall_design: Illumina Infinium MethylationEPIC BeadChip (850k) array analysis of 3 NCCIT and 3 2102EP clones deficient for CD24, 1 parental control each


title: Integrative genome-wide analysis of dopaminergic neuron-specific PARIS expression in Drosophila dissects recognition of multiple PPAR-γ associated gene regulation

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens


title: piRNA pathway is essential for generating functional oocytes in golden hamster

first: Fengjuan

last: Zhang

state: Shanghai

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

country: China

institute: Shanghai Institutes for Biological Sciences, CAS

summary: Piwi-interacting RNAs (piRNAs) are small RNAs predominantly expressed in germ cells that function in gametogenesis in various species. Notably, PIWI-deficient female mice are fertile and mouse oocytes express a panel of small RNAs that do not appear widely representative of mammals. Thus, the function of piRNAs in mammalian oogenesis remains largely elusive. Here, we generated PIWIL1- and MOV10L1-deficient golden hamsters and found that all female and male mutants were sterile, with severe defects in embryogenesis and spermatogenesis, respectively. PIWIL1-deficient oocytes displayed aberrant transposon accumulation and broad transcriptomic dysregulation, and maternal PIWIL1-deficient embryos had impaired zygotic genome activation (ZGA). Moreover, our results support that PIWIL1-piRNAs exert a non-redundant function in silencing endogenous retroviruses (ERVs) in oocytes. Together, our findings demonstrate that piRNAs are indispensable for generating functional germ cells in golden hamsters and show the informative value of this model species for functional and mechanistic investigations of piRNAs in gametogenesis, especially those related to female infertility.

overall_design: Small and long RNAs profiling of developing oocytes and early embryos in wild-type and PIWIL1-deficient golden hamster females, as well as profiling of smRNAs after oxidation or PIWIL1- and PIWIL3-IP in MII stage oocytes or testis of wild-types and PIWIL1-mutents.

first: Hongdao

first: Jinghua

last: Chen

first: Mingzhi

last: Li

first: Xiaolong

last: Lv

first: Yali

last: Xiao

first: Zhaozhen

first: Li

last: Hou

first: Yana

last: Lai

first: Ying

first: Wen

first: Aihua

first: Shiqi

last: Gao

first: Heling

last: Fu

first: Jianli

last: Zhou

first: Feiyang

last: Diao

first: Aimin

last: Shi

first: Youqiang

last: Su

first: Wentao

last: Zeng

first: Ligang

last: Wu

first: Jianmin

first: Siqi


title: Integrative genome-wide analysis of dopaminergic neuron-specific PARIS expression dissects recognition of multiple PPAR-γ associated gene regulation (TRAP-Seq).

first: Karin

last: Danzer

summary: PURPOSE: The transcriptional repressor PARIS (ZNF746) was initially identified as a pathogenic co-substrate of PINK1 and parkin that leads to Parkinson’s disease (PD) by disrupting mitochondrial biogenesis through PPARγ coactivator -1α (PGC-1α) suppression. Later, accumulation of PARIS in dopamine (DA) neurons that cause neurotoxicity has been studied widely and growing evidence has linked defective mitochondrial biogenesis to PD pathogenesis. Yet, the mechanistic underpinnings of this link remain elusive. METHODS: We employed translating ribosome affinity purification (TRAP) followed by RNA sequencing (TRAP-seq) for transcriptome profiling of DA neurons in transgenic Drosophila lines we generated expressing human PARIS or human PARIS mutant (C571A). Together with TRAP control and whole brain samples, this data set is composed of a total of 10 (3, 3, 3, and 1 respectively) replicate samples representing 4 different treatment groups for a set of gene-level (a parametric F-test) and transcript-level (a Wald test or a likelihood ratio test) differential expression analysis. RESULTS: Firstly, we identified differentially expressed genes by human PARIS in fly DA neurons successfully. Then, we showed that PPARγ acts as a master regulator of transcriptomic changes induced by PARIS in the clusters of Drosophila dopaminergic neurons. Also, we validated this finding in human neuroblastoma cell line. CONCLUSION: PPARγ plays a crucial regulatory role in PARIS phenotype. Drosophila models of PARIS-induced neurodegeneration used in this work to represent PD phenotype and our TRAP-seq protocol serve as a paradigm for future studies to unravel mechanistic underpinnings of PARIS biology.

overall_design: TRAP control (3X), PARIS wild type (3X), PARIS mutant (C571A) (3X), and whole brain (1X) samples, adding up to a total of 10 replicate samples representing 4 different groups. Whole brain serves as a control for TRAP enrichment. TRAP control serves as a control for PARIS transgenic constructs.

first: Sung

last: Kang

first: Volkan

last: Yazar


title: Genome-wide maps of ERα-bound RNAs and ERα-DNA binding events

city: Hangzhou

first: Yichen

last: Xu

address: Yuhangtang Road 866

institute: Zhejiang University


title: Genome-wide maps of ERα-DNA binding events

summary: To identify WT and RNA-binding-domain-mutated (RBDmut) ERα binding sites on DNA, we performed ChIP-seq of FLAG-tagged ERα.

overall_design: The endogenous ERα in MCF7 cells were replaced with equal amount of WT and RBDmut FLAG-tagged ERα, and cells were subjected to the ChIP-seq procedure.

first: Y

first: D

last: Ruggero


title: RNA sequencing data of NCCIT cells deficient for CD24 and parental controls

first: Daniel

last: Nettersheim

summary: Single eng 3' RNA sequencing of embryonal carcinoma cell line NCCIT deficient for CD24 and parental cells. CD24 deficiency was genereted by CRISPR/Cas9 method. Five different NCCIT knock out clones were sequenced.

overall_design: RNA sequencing of 5 NCCIT clones deficient for CD24, 2 parental control